VMD - Visual Molecular Dynamics - Quick Help

Help is available for the following topics:

  1. VMD Text Commands
  2. VMD Command-Line Options
  3. VMD Environment Variables

For the latest news about VMD, please see the VMD home page. VMD is one component of the MDScope software, which includes also the program NAMD (a portable, parallel molecular dynamics program) and the MDCOMM software to enable communication betweenVMD and NAMD. For further information on MDScope, please see the Theoretical Biophysics group home page.

For a complete description on how to install, use, or modify VMD, please see the VMD Installation Guide, the VMD User's Guide, or the VMD Programmer's Guide.

Please send bug reports, comments, or suggestions to vmd@ks.uiuc.edu.

VMD Text Command Summary

VMD understands commands which start with the following words; click on a command for a more complete synopsis. Items marked as (optional) may not be available in the current version of VMD.

VMD Text Command Descriptions

Words which complete the command are shown in the sublist. Optional arguments are enclosed by [ ]. Option lists are denoted by < a | b | c >. Dummy arguments are shown like this.

VMD Command-Line Option Summary

When started, the following command-line parameters may be given to VMD. Note that if a command-line parameter does not start with a dash (-), and is not part of another option, it is assumed to be a PDB filename. Thus, the command
vmd molecule.pdb
will start VMD and load a molecule from the file molecule.pdb.
-? | -h
Print a summary a command-line options to the console.
-e filename
After initialization, execute the text commands in filename, and then resume normal operation.
-psf filename
Load the specified molecule (in PSF format) at startup. The PSF file only contains the molecular structure; a PDB or DCD file must also be specified when this option is used.
-pdb filename
Load the specified molecule (in PDB format) at startup.
-dcd filename
Load the specified trajectory file (in binary DCD format) at startup. The DCD file only contains atomic coordinates; a PDB or PSF file must also be specified when this option is used.
-disp < win | text | cave | none >
Specify the type of graphical display to use. The possible display devices include: It is possible to use VMD as a filter to convert coordinate files into rendered images, by using the -disp text and -e options.
-pos x y
Specify the position for the graphics display window. The position (x,y) is the number of pixels from the lower-left corner of the display to the lower-left corner of the graphics window.
-size x y
Specify the size for the graphics display window, in pixels.
Do not display the VMD title at startup.
-startup filename
Use filename as the VMD startup command script, instead of the default file.
-init filename
Use filename as the file containing VMD initialization data, instead of the default file.
-debug [level]
Turn on output of debugging messages, and optionally set the current debug level (1=few messages ... 5=many verbose messages). Note this is only useful if VMD has been compiled with debugging message included.

VMD Environment Variable Summary

Several environment variables are used by VMD to determine the location of certain files and directories. These variables include:
The directory which contains the VMD data files (such as this help file) and architecture-specific executables. By default, this is /usr/local/lib/vmd.
The directory which VMD should use for temporary data files. By default, this is /tmp.
The complete path and filename for the program babel, which is used by VMD to convert molecular structure/coordinates files into PDB files which VMD can actually understand. If this is not set explicitly, the VMD startup script will attempt to find babel in the current path. If babel cannot be found or is not installed, VMD will not be able to read molecular file formats other than PDB, PSF, and binary DCD files. The program babel may be obtained via anonymous ftp from the University of Arizona Biotechnology ftp server, joplin.biosci.arizona.edu.
The name of the HTML viewer (Netscape, Mosaic, whatever you prefer) that VMD should use to display HTML documents (such as this help file). By default, this is Mosaic (hey, we are at the University of Illinois, NCSA is literally right upstairs ...).

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VMD Documentation / Theoretical Biophysics Group, University of Illinois / vmd@ks.uiuc.edu